Approach:
We propose to leverage emerging and standard computational and experimental approaches, building on existing and newly developed resources to support stewardship of plant genome reference sequences, genome annotations and gene networks. This will support development of a common standard platform for comparative genomic analysis and visualization. The enriched genome annotations will include controlled vocabularies to describe metadata and primary data associated with comparative phylogenomics, epigenetics, and population-based phenotypes.
The proposed research in gene networks is directed at the development and validation of gene regulatory networks (GRN). The network view of the underlying molecular processes will enhance the fundamental biological understanding of development and abiotic stress responses and its relationship to agronomic traits. The computationally predicted and experimentally verified sub-networks combined with the prioritized regulatory gene targets will provide focal points for further research at gene-by-gene level. They will be integrated with the suite of genetic resources obtained from Objective 1, including SNPs and orthology mapping, and thus will be a resource for breeders and researchers engaged in molecular breeding approaches and segregation analysis. Genome-wide network reconstructions will be quite useful in quantifying and characterizing the genotype-to-phenotype relationships.
We propose to leverage and build upon existing infrastructure to manage and analyze plant genomic, genetic, and phenotypic data. The resources will focus on the delivery of anticipated products from Objectives 1 and 2 with a focus on plant datasets, but much of the software will be species-agnostic, making the resources developed from the project usable to a broader audience including animals, insects, and fish relevant to agriculture, human health, and a sustainable environment.